Joanne:

1. There is no mechanism for downloading reference sequences from Galaxy at 
this time.
2. I am not sure what you mean by 'Tablet'.
3. Megablast tool ('NGS: Mapping -> Megablast') will allow you to perform 
comparisons against nt, wgs, and htgs databases.

Thanks for using Galaxy,

anton
galaxy team


Anton Nekrutenko
http://nekrut.bx.psu.edu
http://usegalaxy.org



On Jun 22, 2011, at 4:15 PM, Joanne Rampersad wrote:

> Hi
> I have a few questions
> 
> 1. I am trying to use Bowtie to map my data using a reference genome.
> the genome is available on Galaxy (Escherichia coli DH10B (20079)). Is
> there a way that I can download the file in fasta format to use as a
> reference in Tablet?
> 
> I can import the SAM output into Tablet if I do not give it a
> reference, but I would like to see it with the reference
> 
> 2. I have used the Sam to Bam converter and downloaded the file to my
> computer then tried to import it into Tablet, but it gives an error.
> Does anyone have any advice on doing this?
> 
> 3. Does Galaxy have any tools for doing a blast search against a
> reference genome or database?
> 
> Any help/instructions that you point me to is greatly appreciated.
> 
> 
> Jo
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